| tags: [ Genomic Data GWAS ] categories: [Coding Experiments ]
Annotating signficant GWAS hits
Introduction
The pedigree-based GWAS identified 9 heritable traits with significant hits (i.e. SNPs that pass genome-wide significance threshold, p < 1.84e-7). The number of significant hits within each trait highly varied. To identify the most robust hits, SNPs that pass the genome-wide signficance threshold would ideally have adjacent SNPs that pass the suggestive threshold. Therefore, I will attempt to filter the significant hits/loci based on the presence of significant (suggestive) SNPs.
Methods and Results
require(magrittr)
require(dplyr)
require(gaston)
require(qqman)Load relevant data
nies_heritable_pheno <- read.csv('C:/Users/Martha/Documents/Honours/Project/honours.project/Data/nies_heritable_pheno.csv', header = T)
merged_nies_210818 <- read.bed.matrix("C:/Users/Martha/Documents/Honours/Project/honours.project/Data/merged_nies/merged_nies_geno_210818.bed")## Reading C:/Users/Martha/Documents/Honours/Project/honours.project/Data/merged_nies/merged_nies_geno_210818.fam
## Reading C:/Users/Martha/Documents/Honours/Project/honours.project/Data/merged_nies/merged_nies_geno_210818.bim
## Reading C:/Users/Martha/Documents/Honours/Project/honours.project/Data/merged_nies/merged_nies_geno_210818.bed
## ped stats and snps stats have been set.
## 'p' has been set.
## 'mu' and 'sigma' have been set.merged_nies_GRM <- GRM(merged_nies_210818)
merged_nies_eiK <- eigen(merged_nies_GRM)
merged_nies_eiK$values[ merged_nies_eiK$values < 0] <- 0
merged_nies_PC <- sweep(merged_nies_eiK$vectors, 2, sqrt(merged_nies_eiK$values), "*")1. Perform GWAS
r_kvalV_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$R.K.value.V, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
r_kvalV_gwas <- na.omit(r_kvalV_gwas)
head(r_kvalV_gwas)## chr pos id A1 A2 freqA2 h2 LRT p
## 1 1 590318 rs2808353 G A 0.9855072 0.7605548 1.258239e-03 0.9717036
## 2 1 778897 rs138660747 A C 0.9956522 0.7609519 1.877719e-02 0.8910072
## 3 1 783175 rs10751453 T C 1.0000000 0.7608180 1.195986e-10 0.9999913
## 4 1 804046 rs3131973 A G 1.0000000 0.7608180 -1.864464e-10 1.0000000
## 5 1 817186 rs3094315 G A 0.8333333 0.7542221 6.438475e-01 0.4223210
## 6 1 833068 rs12562034 A G 0.8695652 0.7608423 1.138512e-05 0.9973078r_kvalV_filtered <- r_kvalV_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)2. Identify significant hits (passing genome-wide threshold)
r_kvalV_meff <- r_kvalV_filtered %>% filter(p < 1.84e-7)
head(r_kvalV_meff)## chr pos id A1 A2 freqA2 h2 LRT p
## 1 1 205916931 rs60255052 C T 0.9811594 0.6398584 34.38041 4.532633e-09
## 2 1 205920201 rs16856470 T C 0.9811594 0.6398584 34.38041 4.532633e-09
## 3 1 205920404 rs16856473 A G 0.9811594 0.6398584 34.38041 4.532633e-09
## 4 1 205936240 rs1473537 T C 0.9739130 0.6448387 28.29076 1.043931e-07
## 5 4 119235738 rs78341058 A T 0.9855072 0.6858759 28.47085 9.511997e-08
## 6 4 119240001 rs79063845 C T 0.9855072 0.6858759 28.47085 9.511997e-08113 SNPs pass genome-wide threshold.
3. Identify the most significant SNP per chromosome
r_kvalV_sig <- do.call(rbind, lapply(split(r_kvalV_meff,r_kvalV_meff$chr), function(x) {return(x[which.min(x$p),])}))
head(r_kvalV_sig)## chr pos id A1 A2 freqA2 h2 LRT
## 1 1 205920404 rs16856473 A G 0.9811594 0.6398584 34.38041
## 4 4 119403429 rs112414671 A G 0.9869565 0.6769095 30.96024
## 15 15 57746156 rs143347058 A G 0.9898551 0.7970430 28.28088
## p
## 1 4.532633e-09
## 4 2.633682e-08
## 15 1.049275e-073 SNPs are identified (chr 1, 4, 15).
4. Determine number of significant SNPs within 100kb of most significant hits
r_kvalV_res <- NULL
for (i in r_kvalV_sig$id) {
snpID <- i
snpCHR <- r_kvalV_filtered[r_kvalV_filtered$id == snpID,]$chr
snpPOS <- r_kvalV_filtered[r_kvalV_filtered$id ==snpID,]$pos
sig.peak <- r_kvalV_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
r_kvalV_res <- rbind(r_kvalV_res, sig.peak)
}
r_kvalV_res## chr pos id A1 A2 freqA2 h2 LRT
## 1 1 205916566 rs72752923 C A 0.9782609 0.6943696 24.25721
## 2 1 205916729 rs16830364 G A 0.9782609 0.6943696 24.25721
## 3 1 205916931 rs60255052 C T 0.9811594 0.6398584 34.38041
## 4 1 205917041 rs60716530 C T 0.9782609 0.6943696 24.25721
## 5 1 205917115 rs60644810 G A 0.9782609 0.6943696 24.25721
## 6 1 205917248 rs35694044 A T 0.9782609 0.6943696 24.25721
## 7 1 205917652 rs16830370 T C 0.9782609 0.6943696 24.25721
## 8 1 205918853 rs16856462 C T 0.9782609 0.6943696 24.25721
## 9 1 205919195 rs16856468 G A 0.9782609 0.6943696 24.25721
## 10 1 205919303 rs60001177 T C 0.9782609 0.6943696 24.25721
## 11 1 205919401 rs12723666 A G 0.9782609 0.6943696 24.25721
## 12 1 205920201 rs16856470 T C 0.9811594 0.6398584 34.38041
## 13 1 205920404 rs16856473 A G 0.9811594 0.6398584 34.38041
## 14 1 205922403 rs68189466 G A 0.9797101 0.6457784 26.64533
## 15 1 205922720 rs35648260 G T 0.9797101 0.6457784 26.64533
## 16 1 205922775 rs35360452 G T 0.9797101 0.6457784 26.64533
## 17 1 205925474 rs12727528 A G 0.9797101 0.6457784 26.64533
## 18 1 205935183 rs1891309 G A 0.9782609 0.6459447 23.46813
## 19 1 205935330 rs1891310 T G 0.9782609 0.6459447 23.46813
## 20 1 205936240 rs1473537 T C 0.9739130 0.6448387 28.29076
## 21 1 205942026 rs72752928 T C 0.9782609 0.6459447 23.46813
## 22 1 205943691 rs66593238 T C 0.9782609 0.6459447 23.46813
## 23 1 205944627 rs9438407 T G 0.9782609 0.6459447 23.46813
## 24 1 205945388 rs12741299 T C 0.9782609 0.6459447 23.46813
## 25 1 205946647 rs34265780 T C 0.9782609 0.6459447 23.46813
## 26 4 119362510 rs112314510 A G 0.9855072 0.6858759 28.47085
## 27 4 119362552 rs111968273 T A 0.9855072 0.6858759 28.47085
## 28 4 119367677 rs113059419 A G 0.9869565 0.6769095 30.96024
## 29 4 119372303 rs112760591 G A 0.9855072 0.6858759 28.47085
## 30 4 119372480 rs111609258 C G 0.9855072 0.6858759 28.47085
## 31 4 119378224 rs147602981 G A 0.9855072 0.6858759 28.47085
## 32 4 119381167 rs143847948 A C 0.9855072 0.6858759 28.47085
## 33 4 119390257 rs113224532 T C 0.9855072 0.6858759 28.47085
## 34 4 119392279 rs117856633 C A 0.9855072 0.6858759 28.47085
## 35 4 119398681 rs113825627 C G 0.9855072 0.6858759 28.47085
## 36 4 119403429 rs112414671 A G 0.9869565 0.6769095 30.96024
## 37 4 119404439 rs183181597 A G 0.9855072 0.6858759 28.47085
## 38 4 119404927 rs113317707 C A 0.9855072 0.6858759 28.47085
## 39 4 119408454 rs184703141 T C 0.9855072 0.6858759 28.47085
## 40 15 57746156 rs143347058 A G 0.9898551 0.7970430 28.28088
## p
## 1 8.429104e-07
## 2 8.429104e-07
## 3 4.532633e-09
## 4 8.429104e-07
## 5 8.429104e-07
## 6 8.429104e-07
## 7 8.429104e-07
## 8 8.429104e-07
## 9 8.429104e-07
## 10 8.429104e-07
## 11 8.429104e-07
## 12 4.532633e-09
## 13 4.532633e-09
## 14 2.444408e-07
## 15 2.444408e-07
## 16 2.444408e-07
## 17 2.444408e-07
## 18 1.270004e-06
## 19 1.270004e-06
## 20 1.043931e-07
## 21 1.270004e-06
## 22 1.270004e-06
## 23 1.270004e-06
## 24 1.270004e-06
## 25 1.270004e-06
## 26 9.511997e-08
## 27 9.511997e-08
## 28 2.633682e-08
## 29 9.511997e-08
## 30 9.511997e-08
## 31 9.511997e-08
## 32 9.511997e-08
## 33 9.511997e-08
## 34 9.511997e-08
## 35 9.511997e-08
## 36 2.633682e-08
## 37 9.511997e-08
## 38 9.511997e-08
## 39 9.511997e-08
## 40 1.049275e-0740 SNPs are identified. Supporting SNPs are present for peaks/index SNPs on chr 1 and 4, but not index SNP on chr 1. This suggests that “true” peak is present on chr 1 and 4, but not on chr 15.
5. Repeat filtering for 8 other significant traits
Component 8
pc8_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$coord.Dim.8, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
pc8_gwas <- na.omit(pc8_gwas)
pc8_filtered <- pc8_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
pc8_meff <- pc8_filtered %>% filter(p < 1.84e-7)
pc8_sig <- do.call(rbind, lapply(split(pc8_meff,pc8_meff$chr), function(x) {return(x[which.min(x$p),])}))
pc8_res <- NULL
for (i in pc8_sig$id) {
snpID <- i
snpCHR <- pc8_filtered[pc8_filtered$id == snpID,]$chr
snpPOS <- pc8_filtered[pc8_filtered$id ==snpID,]$pos
sig.peak <- pc8_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
pc8_res <- rbind(pc8_res, sig.peak)
}
pc8_res## chr pos id A1 A2 freqA2 h2 LRT p
## 1 9 108296877 rs10979308 A T 0.8072464 0.1474737 21.75750 3.093782e-06
## 2 9 108299426 rs1885973 T A 0.7768116 0.1112269 27.23573 1.800994e-07
## 3 9 108300235 rs10816656 G A 0.7826087 0.1227419 24.32919 8.119906e-07
## 4 9 108302318 rs1407849 T A 0.8057971 0.1476383 22.09787 2.590977e-06
## 5 9 108305442 rs16912866 G A 0.7768116 0.1112269 27.23573 1.800994e-07
## 6 9 108305644 rs16912868 G A 0.7768116 0.1112269 27.23573 1.800994e-07
## 7 9 108306203 rs1323384 A C 0.8086957 0.1451738 21.23098 4.071293e-06
## 8 9 108307394 rs7030371 G A 0.7768116 0.1112269 27.23573 1.800994e-078 SNPs pass genome-wide significance, 1 index SNP identified (chr 9), 7 SNPs support the index.
L ACD
l_acd_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$L.AC.Depth, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
l_acd_gwas <- na.omit(l_acd_gwas)
l_acd_filtered <- l_acd_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
l_acd_meff <- l_acd_filtered %>% filter(p < 1.84e-7)
l_acd_sig <- do.call(rbind, lapply(split(l_acd_meff,l_acd_meff$chr), function(x) {return(x[which.min(x$p),])}))
l_acd_res <- NULL
for (i in l_acd_sig$id) {
snpID <- i
snpCHR <- l_acd_filtered[l_acd_filtered$id == snpID,]$chr
snpPOS <- l_acd_filtered[l_acd_filtered$id ==snpID,]$pos
sig.peak <- l_acd_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
l_acd_res <- rbind(l_acd_res, sig.peak)
}
l_acd_res## chr pos id A1 A2 freqA2 h2 LRT p
## 1 11 87921800 rs17151049 C T 0.9362319 0.09781317 32.60941 1.12668e-0824 SNPs pass genome-wide significance, 1 index SNP identified (chr 11), no supporting SNPs.
L CDR
l_cdr_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$L.CDR, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
l_cdr_gwas <- na.omit(l_cdr_gwas)
l_cdr_filtered <- l_cdr_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
l_cdr_meff <- l_cdr_filtered %>% filter(p < 1.84e-7)
l_cdr_sig <- do.call(rbind, lapply(split(l_cdr_meff,l_cdr_meff$chr), function(x) {return(x[which.min(x$p),])}))
l_cdr_res <- NULL
for (i in l_cdr_sig$id) {
snpID <- i
snpCHR <- l_cdr_filtered[l_cdr_filtered$id == snpID,]$chr
snpPOS <- l_cdr_filtered[l_cdr_filtered$id ==snpID,]$pos
sig.peak <- l_cdr_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
l_cdr_res <- rbind(l_cdr_res, sig.peak)
}
l_cdr_res## chr pos id A1 A2 freqA2 h2 LRT p
## 1 4 52923518 rs115266839 A G 0.9884058 0.6932395 29.62028 5.255231e-08
## 2 17 67425699 rs191190284 T A 0.9869565 0.7451182 29.32129 6.131843e-082 SNPs pass genome-wide significance, 2 index SNPs identified (chr 4, 17), no supporting peaks
L K-value H
l_KvalH_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$L.K.value.H, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
l_KvalH_gwas <- na.omit(l_KvalH_gwas)
l_kvalH_filtered <- l_KvalH_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
l_kvalH_meff <- l_kvalH_filtered %>% filter(p < 1.84e-7)
l_kvalH_sig <- do.call(rbind, lapply(split(l_kvalH_meff,l_kvalH_meff$chr), function(x) {return(x[which.min(x$p),])}))
l_kvalH_res <- NULL
for (i in l_kvalH_sig$id) {
snpID <- i
snpCHR <- l_kvalH_filtered[l_kvalH_filtered$id == snpID,]$chr
snpPOS <- l_kvalH_filtered[l_kvalH_filtered$id ==snpID,]$pos
sig.peak <- l_kvalH_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
l_kvalH_res <- rbind(l_kvalH_res, sig.peak)
}
l_kvalH_res## chr pos id A1 A2 freqA2 h2 LRT
## 1 2 32321350 rs148319856 C A 0.9826087 0.22244002 33.29515
## 2 2 32367072 rs115270434 C A 0.9855072 0.17567169 20.65630
## 3 3 77739700 rs1163757 A G 0.9869565 0.03021585 32.17915
## 4 6 82442490 rs114928787 T C 0.9855072 0.00000000 43.16564
## 5 6 82442833 rs116172930 C A 0.9855072 0.00000000 43.16564
## 6 6 82443802 rs74436554 C T 0.9855072 0.00000000 43.16564
## 7 6 82444791 rs78056249 C G 0.9855072 0.00000000 43.16564
## 8 6 82445716 rs77941466 C T 0.9855072 0.00000000 43.16564
## 9 6 82447004 rs116461493 T C 0.9855072 0.00000000 43.16564
## 10 6 82447732 rs77666578 G A 0.9855072 0.00000000 43.16564
## 11 6 82451563 rs75189229 A G 0.9855072 0.00000000 43.16564
## 12 6 82453938 rs117178778 A G 0.9855072 0.00000000 43.16564
## 13 6 82454058 rs116246536 T G 0.9855072 0.00000000 43.16564
## 14 6 82454140 rs78427866 A G 0.9855072 0.00000000 43.16564
## 15 6 82454380 rs147257041 A G 0.9855072 0.00000000 43.16564
## 16 6 82454449 rs140711073 T C 0.9855072 0.00000000 43.16564
## 17 6 82454505 rs142248448 T C 0.9855072 0.00000000 43.16564
## 18 6 82454620 rs114442506 A G 0.9855072 0.00000000 43.16564
## 19 6 82456537 rs145558293 A G 0.9855072 0.00000000 43.16564
## 20 6 82458393 rs77391407 C T 0.9855072 0.00000000 43.16564
## 21 6 82458546 rs77103853 G C 0.9855072 0.00000000 43.16564
## 22 6 82459011 rs115096710 T C 0.9855072 0.00000000 43.16564
## 23 6 82459713 rs77245672 G C 0.9855072 0.00000000 43.16564
## 24 6 82459810 rs77599496 T A 0.9855072 0.00000000 43.16564
## 25 6 82459890 rs77598967 G A 0.9855072 0.00000000 43.16564
## 26 6 82460167 rs115847999 C G 0.9855072 0.00000000 43.16564
## 27 6 82460379 rs116730626 G A 0.9855072 0.00000000 43.16564
## 28 6 82460650 rs149355051 G T 0.9855072 0.00000000 43.16564
## 29 6 82462126 rs76856243 T C 0.9855072 0.00000000 43.16564
## 30 6 82462603 rs6933239 C T 0.9855072 0.00000000 43.16564
## 31 6 82462992 rs6911216 A C 0.9855072 0.00000000 43.16564
## 32 6 82465617 rs6928806 A C 0.9855072 0.00000000 43.16564
## 33 6 82466574 rs74404091 C T 0.9855072 0.00000000 43.16564
## 34 6 82466715 rs79358384 G A 0.9855072 0.00000000 43.16564
## 35 6 82467200 rs77721025 A C 0.9855072 0.00000000 43.16564
## 36 6 82467706 rs116423281 A G 0.9855072 0.00000000 43.16564
## 37 6 82467953 rs142216660 T C 0.9855072 0.00000000 43.16564
## 38 6 82467988 rs140099919 A G 0.9855072 0.00000000 43.16564
## 39 6 82468668 rs78941585 G A 0.9855072 0.00000000 43.16564
## 40 6 82468774 rs75228268 A T 0.9855072 0.00000000 43.16564
## 41 6 82469116 rs77552654 T A 0.9855072 0.00000000 43.16564
## 42 6 82470649 rs149706908 G T 0.9855072 0.00000000 43.16564
## 43 6 82470651 rs144623191 T C 0.9855072 0.00000000 43.16564
## 44 6 82470859 rs192614396 C A 0.9855072 0.00000000 43.16564
## 45 6 82471119 rs151156468 C T 0.9855072 0.00000000 43.16564
## 46 6 82471338 rs140554533 A G 0.9855072 0.00000000 43.16564
## 47 6 82471381 rs150446760 C G 0.9855072 0.00000000 43.16564
## 48 6 82471679 rs138339145 T C 0.9855072 0.00000000 43.16564
## 49 6 82472140 rs142089466 T C 0.9855072 0.00000000 43.16564
## 50 6 82473676 rs147151928 G C 0.9855072 0.00000000 43.16564
## 51 6 82473679 rs140298049 C T 0.9855072 0.00000000 43.16564
## 52 6 82473688 rs149655171 A G 0.9855072 0.00000000 43.16564
## 53 6 82474468 rs146864360 T C 0.9855072 0.00000000 43.16564
## 54 6 82474648 rs140520501 C T 0.9855072 0.00000000 43.16564
## 55 6 82474867 rs150394443 T C 0.9855072 0.00000000 43.16564
## 56 6 82475320 rs143579868 A T 0.9855072 0.00000000 43.16564
## 57 6 82475696 rs115741750 C T 0.9855072 0.00000000 43.16564
## 58 6 82477810 rs77406497 T C 0.9855072 0.00000000 43.16564
## 59 6 82478378 rs115813741 T G 0.9855072 0.00000000 43.16564
## 60 6 82478650 rs78900243 G A 0.9855072 0.00000000 43.16564
## 61 6 82478870 rs76557363 T G 0.9855072 0.00000000 43.16564
## 62 6 82479264 rs77943130 T G 0.9855072 0.00000000 43.16564
## 63 6 82479546 rs115245280 A G 0.9855072 0.00000000 43.16564
## 64 6 82479664 rs75910615 A G 0.9855072 0.00000000 43.16564
## 65 6 82480370 rs76438934 A G 0.9855072 0.00000000 43.16564
## 66 6 82481986 rs115034961 A C 0.9855072 0.00000000 43.16564
## 67 6 82482183 rs79967481 G A 0.9855072 0.00000000 43.16564
## 68 6 82482254 rs116699765 T C 0.9855072 0.00000000 43.16564
## 69 6 82483125 rs78639250 T C 0.9855072 0.00000000 43.16564
## 70 6 82483522 rs75763492 A G 0.9855072 0.00000000 43.16564
## 71 6 82483898 rs76617768 T C 0.9855072 0.00000000 43.16564
## 72 6 82484287 rs76652063 C A 0.9855072 0.00000000 43.16564
## 73 6 82484758 rs114024754 A G 0.9855072 0.00000000 43.16564
## 74 6 82485370 rs79031996 C G 0.9855072 0.00000000 43.16564
## 75 6 82485916 rs77517398 C T 0.9855072 0.00000000 43.16564
## 76 6 82486863 rs80252551 A T 0.9855072 0.00000000 43.16564
## 77 6 82488997 rs114963095 G T 0.9855072 0.00000000 43.16564
## 78 6 82489053 rs77561386 C T 0.9855072 0.00000000 43.16564
## 79 6 82489164 rs76602861 A G 0.9855072 0.00000000 43.16564
## 80 6 82490178 rs79435750 A G 0.9855072 0.00000000 43.16564
## 81 6 82490367 rs80347071 C G 0.9855072 0.00000000 43.16564
## 82 6 82492170 rs74785531 C T 0.9855072 0.00000000 43.16564
## 83 6 82492233 rs74361967 C T 0.9855072 0.00000000 43.16564
## 84 6 82492321 rs75373608 A T 0.9855072 0.00000000 43.16564
## 85 10 64099069 rs74804993 G A 0.9826087 0.27726310 31.54649
## 86 16 13935176 rs1800067 A G 0.9550725 0.29435196 33.85516
## p
## 1 7.917990e-09
## 2 5.495605e-06
## 3 1.405911e-08
## 4 5.029621e-11
## 5 5.029621e-11
## 6 5.029621e-11
## 7 5.029621e-11
## 8 5.029621e-11
## 9 5.029621e-11
## 10 5.029621e-11
## 11 5.029621e-11
## 12 5.029621e-11
## 13 5.029621e-11
## 14 5.029621e-11
## 15 5.029621e-11
## 16 5.029621e-11
## 17 5.029621e-11
## 18 5.029621e-11
## 19 5.029621e-11
## 20 5.029621e-11
## 21 5.029621e-11
## 22 5.029621e-11
## 23 5.029621e-11
## 24 5.029621e-11
## 25 5.029621e-11
## 26 5.029621e-11
## 27 5.029621e-11
## 28 5.029621e-11
## 29 5.029621e-11
## 30 5.029621e-11
## 31 5.029621e-11
## 32 5.029621e-11
## 33 5.029621e-11
## 34 5.029621e-11
## 35 5.029621e-11
## 36 5.029621e-11
## 37 5.029621e-11
## 38 5.029621e-11
## 39 5.029621e-11
## 40 5.029621e-11
## 41 5.029621e-11
## 42 5.029621e-11
## 43 5.029621e-11
## 44 5.029621e-11
## 45 5.029621e-11
## 46 5.029621e-11
## 47 5.029621e-11
## 48 5.029621e-11
## 49 5.029621e-11
## 50 5.029621e-11
## 51 5.029621e-11
## 52 5.029621e-11
## 53 5.029621e-11
## 54 5.029621e-11
## 55 5.029621e-11
## 56 5.029621e-11
## 57 5.029621e-11
## 58 5.029621e-11
## 59 5.029621e-11
## 60 5.029621e-11
## 61 5.029621e-11
## 62 5.029621e-11
## 63 5.029621e-11
## 64 5.029621e-11
## 65 5.029621e-11
## 66 5.029621e-11
## 67 5.029621e-11
## 68 5.029621e-11
## 69 5.029621e-11
## 70 5.029621e-11
## 71 5.029621e-11
## 72 5.029621e-11
## 73 5.029621e-11
## 74 5.029621e-11
## 75 5.029621e-11
## 76 5.029621e-11
## 77 5.029621e-11
## 78 5.029621e-11
## 79 5.029621e-11
## 80 5.029621e-11
## 81 5.029621e-11
## 82 5.029621e-11
## 83 5.029621e-11
## 84 5.029621e-11
## 85 1.947216e-08
## 86 5.937145e-09147 SNPs pass genome-wide significance, 5 index SNPs identified (chr 2, 3,6, 10, 16), supporting SNPs identified for index SNPs on chr 2 and 6.
Component 3
pc3_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$coord.Dim.3, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
pc3_gwas <- na.omit(pc3_gwas)
pc3_filtered <- pc3_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
pc3_meff <- pc3_filtered %>% filter(p < 1.84e-7)
pc3_sig <- do.call(rbind, lapply(split(pc3_meff,pc3_meff$chr), function(x) {return(x[which.min(x$p),])}))
pc3_res <- NULL
for (i in pc3_sig$id) {
snpID <- i
snpCHR <- pc3_filtered[pc3_filtered$id == snpID,]$chr
snpPOS <- pc3_filtered[pc3_filtered$id ==snpID,]$pos
sig.peak <- pc3_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
pc3_res <- rbind(pc3_res, sig.peak)
}
pc3_res## chr pos id A1 A2 freqA2 h2 LRT
## 1 1 205916566 rs72752923 C A 0.9782609 0.10018393 32.70563
## 2 1 205916729 rs16830364 G A 0.9782609 0.10018393 32.70563
## 3 1 205916931 rs60255052 C T 0.9811594 0.06871623 39.43647
## 4 1 205917041 rs60716530 C T 0.9782609 0.10018393 32.70563
## 5 1 205917115 rs60644810 G A 0.9782609 0.10018393 32.70563
## 6 1 205917248 rs35694044 A T 0.9782609 0.10018393 32.70563
## 7 1 205917652 rs16830370 T C 0.9782609 0.10018393 32.70563
## 8 1 205918853 rs16856462 C T 0.9782609 0.10018393 32.70563
## 9 1 205919195 rs16856468 G A 0.9782609 0.10018393 32.70563
## 10 1 205919303 rs60001177 T C 0.9782609 0.10018393 32.70563
## 11 1 205919401 rs12723666 A G 0.9782609 0.10018393 32.70563
## 12 1 205920201 rs16856470 T C 0.9811594 0.06871623 39.43647
## 13 1 205920404 rs16856473 A G 0.9811594 0.06871623 39.43647
## 14 1 205922403 rs68189466 G A 0.9797101 0.07135981 40.62325
## 15 1 205922720 rs35648260 G T 0.9797101 0.07135981 40.62325
## 16 1 205922775 rs35360452 G T 0.9797101 0.07135981 40.62325
## 17 1 205925474 rs12727528 A G 0.9797101 0.07135981 40.62325
## 18 1 205935183 rs1891309 G A 0.9782609 0.06871632 34.26420
## 19 1 205935330 rs1891310 T G 0.9782609 0.06871632 34.26420
## 20 1 205936240 rs1473537 T C 0.9739130 0.10624855 27.50857
## 21 1 205942026 rs72752928 T C 0.9782609 0.06871632 34.26420
## 22 1 205943691 rs66593238 T C 0.9782609 0.06871632 34.26420
## 23 1 205944627 rs9438407 T G 0.9782609 0.06871632 34.26420
## 24 1 205945388 rs12741299 T C 0.9782609 0.06871632 34.26420
## 25 1 205946647 rs34265780 T C 0.9782609 0.06871632 34.26420
## 26 2 85686354 rs6759832 C T 0.9884058 0.14207905 36.56416
## 27 3 42006157 rs71315517 G C 0.9869565 0.06803235 36.98345
## 28 4 119362510 rs112314510 A G 0.9855072 0.07448922 41.35203
## 29 4 119362552 rs111968273 T A 0.9855072 0.07448922 41.35203
## 30 4 119367677 rs113059419 A G 0.9869565 0.04972603 45.15567
## 31 4 119372303 rs112760591 G A 0.9855072 0.07448922 41.35203
## 32 4 119372480 rs111609258 C G 0.9855072 0.07448922 41.35203
## 33 4 119378224 rs147602981 G A 0.9855072 0.07448922 41.35203
## 34 4 119381167 rs143847948 A C 0.9855072 0.07448922 41.35203
## 35 4 119390257 rs113224532 T C 0.9855072 0.07448922 41.35203
## 36 4 119392279 rs117856633 C A 0.9855072 0.07448922 41.35203
## 37 4 119398681 rs113825627 C G 0.9855072 0.07448922 41.35203
## 38 4 119403429 rs112414671 A G 0.9869565 0.04972603 45.15567
## 39 4 119403485 rs185357281 A G 0.9869565 0.06942631 28.75451
## 40 4 119404439 rs183181597 A G 0.9855072 0.07448922 41.35203
## 41 4 119404927 rs113317707 C A 0.9855072 0.07448922 41.35203
## 42 4 119408454 rs184703141 T C 0.9855072 0.07448922 41.35203
## 43 5 25293191 rs138955515 A G 0.9855072 0.07868229 31.90296
## 44 5 25300269 rs140158697 C T 0.9855072 0.07868229 31.90296
## 45 5 25331088 rs114133913 T A 0.9855072 0.07868229 31.90296
## 46 8 80306741 rs111864836 G T 0.9884058 0.10992188 30.94734
## 47 8 80306859 rs113627660 G C 0.9884058 0.10992188 30.94734
## 48 8 80307293 rs7845792 A G 0.9884058 0.10992188 30.94734
## 49 8 80307388 rs7845575 G A 0.9869565 0.12264506 24.21587
## 50 8 80307700 rs114654811 C T 0.9884058 0.10992188 30.94734
## 51 8 80307701 rs115278078 A T 0.9884058 0.10992188 30.94734
## 52 8 80307837 rs79018076 T C 0.9884058 0.10992188 30.94734
## 53 8 80308098 rs112501384 G C 0.9884058 0.10992188 30.94734
## 54 8 80309305 rs11996376 A G 0.9884058 0.10992188 30.94734
## 55 8 80309598 rs79431653 C G 0.9884058 0.10992188 30.94734
## 56 8 80309626 rs11996450 T C 0.9884058 0.10992188 30.94734
## 57 8 80310193 rs60741023 C G 0.9884058 0.10992188 30.94734
## 58 8 80310485 rs7844286 C T 0.9884058 0.10992188 30.94734
## 59 8 80310716 rs7844696 A T 0.9884058 0.10992188 30.94734
## 60 8 80310720 rs7826434 G A 0.9884058 0.10992188 30.94734
## 61 8 80311242 rs80031189 C T 0.9884058 0.10992188 30.94734
## 62 8 80311252 rs113823684 A G 0.9884058 0.10992188 30.94734
## 63 8 80311329 rs142907856 A G 0.9884058 0.10992188 30.94734
## 64 8 80311457 rs112582272 A G 0.9884058 0.10992188 30.94734
## 65 8 80311580 rs116773209 G A 0.9884058 0.10992188 30.94734
## 66 8 80311736 rs113314270 G T 0.9884058 0.10992188 30.94734
## 67 8 80311838 rs117693425 A G 0.9884058 0.10992188 30.94734
## 68 8 80312291 rs11988873 C T 0.9884058 0.10992188 30.94734
## 69 8 80312345 rs11988904 A T 0.9884058 0.10992188 30.94734
## 70 8 80312623 rs36051398 A C 0.9884058 0.10992188 30.94734
## 71 8 80313751 rs114426401 T C 0.9884058 0.10992188 30.94734
## 72 8 80314228 rs74981396 G A 0.9884058 0.10992188 30.94734
## 73 8 80317028 rs11998344 T G 0.9884058 0.10992188 30.94734
## 74 8 80317208 rs113244900 C T 0.9884058 0.10992188 30.94734
## 75 8 80318583 rs57246091 A G 0.9884058 0.10992188 30.94734
## 76 8 80318643 rs113901603 G A 0.9884058 0.10992188 30.94734
## 77 8 80319691 rs113718590 A G 0.9884058 0.10992188 30.94734
## 78 8 80320713 rs11987997 A G 0.9884058 0.10992188 30.94734
## 79 8 80321002 rs111527437 T A 0.9884058 0.10992188 30.94734
## 80 8 80321694 rs112815920 G C 0.9884058 0.10992188 30.94734
## 81 8 80323890 rs11998156 C A 0.9884058 0.10992188 30.94734
## 82 8 80323964 rs16907573 G A 0.9884058 0.10992188 30.94734
## 83 8 80324156 rs111257240 C T 0.9884058 0.10992188 30.94734
## 84 8 80325047 rs113437388 T C 0.9884058 0.10992188 30.94734
## 85 8 80326033 rs111370206 G A 0.9884058 0.10992188 30.94734
## 86 8 80326935 rs147955676 A G 0.9884058 0.10992188 30.94734
## 87 8 80327442 rs7841095 C T 0.9884058 0.10992188 30.94734
## 88 8 80327549 rs7822828 C A 0.9884058 0.10992188 30.94734
## 89 8 80327732 rs7823481 C G 0.9884058 0.10992188 30.94734
## 90 8 80328450 rs11990649 A G 0.9884058 0.10992188 30.94734
## 91 8 80329801 rs56960849 A G 0.9884058 0.10992188 30.94734
## 92 8 80330197 rs11995624 C T 0.9884058 0.10992188 30.94734
## 93 8 80330467 rs7837761 A G 0.9869565 0.12264506 24.21587
## 94 8 80332180 rs113042618 T C 0.9884058 0.10992188 30.94734
## 95 8 80332423 rs7001142 G T 0.9884058 0.10992188 30.94734
## 96 8 80332520 rs6980915 G A 0.9884058 0.10992188 30.94734
## 97 8 80332901 rs6473220 T C 0.9884058 0.10992188 30.94734
## 98 8 80332907 rs6473221 A G 0.9884058 0.10992188 30.94734
## 99 8 80333316 rs7835862 C T 0.9884058 0.10992188 30.94734
## 100 8 80333340 rs7817696 A G 0.9884058 0.10992188 30.94734
## 101 8 80333506 rs7817634 T C 0.9884058 0.10992188 30.94734
## 102 8 80333599 rs57419267 C T 0.9884058 0.10992188 30.94734
## 103 8 80333823 rs59130219 C T 0.9884058 0.10992188 30.94734
## 104 8 80334098 rs73691385 T A 0.9884058 0.10992188 30.94734
## 105 8 80334328 rs7840559 C T 0.9884058 0.10992188 30.94734
## 106 8 80334334 rs7822177 G A 0.9884058 0.10992188 30.94734
## 107 8 80334582 rs111631456 A G 0.9884058 0.10992188 30.94734
## 108 8 80334982 rs58109903 T C 0.9884058 0.10992188 30.94734
## 109 8 80335583 rs73691388 G A 0.9884058 0.10992188 30.94734
## 110 8 80336124 rs7837108 T C 0.9884058 0.10992188 30.94734
## 111 8 80336300 rs7840857 T G 0.9884058 0.10992188 30.94734
## 112 8 80336310 rs7840861 T G 0.9884058 0.10992188 30.94734
## 113 8 80337292 rs111888115 T C 0.9884058 0.10992188 30.94734
## 114 8 80337308 rs56871558 T C 0.9884058 0.10992188 30.94734
## 115 8 80337408 rs56116331 A G 0.9884058 0.10992188 30.94734
## 116 8 80337443 rs58592997 T C 0.9884058 0.10992188 30.94734
## 117 8 80337629 rs76783901 A G 0.9884058 0.10992188 30.94734
## 118 8 80337634 rs74468856 G A 0.9884058 0.10992188 30.94734
## 119 8 80337985 rs73691394 C A 0.9884058 0.10992188 30.94734
## 120 8 80338076 rs73691395 T C 0.9884058 0.10992188 30.94734
## 121 8 80338219 rs73691397 C G 0.9884058 0.10992188 30.94734
## 122 8 80338255 rs73691398 G A 0.9884058 0.10992188 30.94734
## 123 8 80338835 rs58958046 A G 0.9884058 0.10992188 30.94734
## 124 8 80338910 rs58786240 C T 0.9884058 0.10992188 30.94734
## 125 8 80338955 rs76867788 C T 0.9884058 0.10992188 30.94734
## 126 8 80339017 rs73691399 T C 0.9884058 0.10992188 30.94734
## 127 8 80339217 rs73691400 C G 0.9884058 0.10992188 30.94734
## 128 8 80339959 rs61233095 C A 0.9884058 0.10992188 30.94734
## 129 8 80340238 rs56408864 A T 0.9884058 0.10992188 30.94734
## 130 8 80340749 rs7826667 A G 0.9884058 0.10992188 30.94734
## 131 8 80341236 rs7000592 G C 0.9884058 0.10992188 30.94734
## 132 12 5987972 rs142100550 T G 0.9884058 0.06670431 28.13313
## 133 14 77833818 rs146124823 G A 0.9898551 0.14932850 29.35113
## p
## 1 1.072260e-08
## 2 1.072260e-08
## 3 3.389072e-10
## 4 1.072260e-08
## 5 1.072260e-08
## 6 1.072260e-08
## 7 1.072260e-08
## 8 1.072260e-08
## 9 1.072260e-08
## 10 1.072260e-08
## 11 1.072260e-08
## 12 3.389072e-10
## 13 3.389072e-10
## 14 1.845969e-10
## 15 1.845969e-10
## 16 1.845969e-10
## 17 1.845969e-10
## 18 4.811508e-09
## 19 4.811508e-09
## 20 1.563996e-07
## 21 4.811508e-09
## 22 4.811508e-09
## 23 4.811508e-09
## 24 4.811508e-09
## 25 4.811508e-09
## 26 1.477230e-09
## 27 1.191362e-09
## 28 1.271391e-10
## 29 1.271391e-10
## 30 1.819783e-11
## 31 1.271391e-10
## 32 1.271391e-10
## 33 1.271391e-10
## 34 1.271391e-10
## 35 1.271391e-10
## 36 1.271391e-10
## 37 1.271391e-10
## 38 1.819783e-11
## 39 8.215837e-08
## 40 1.271391e-10
## 41 1.271391e-10
## 42 1.271391e-10
## 43 1.620700e-08
## 44 1.620700e-08
## 45 1.620700e-08
## 46 2.651253e-08
## 47 2.651253e-08
## 48 2.651253e-08
## 49 8.611958e-07
## 50 2.651253e-08
## 51 2.651253e-08
## 52 2.651253e-08
## 53 2.651253e-08
## 54 2.651253e-08
## 55 2.651253e-08
## 56 2.651253e-08
## 57 2.651253e-08
## 58 2.651253e-08
## 59 2.651253e-08
## 60 2.651253e-08
## 61 2.651253e-08
## 62 2.651253e-08
## 63 2.651253e-08
## 64 2.651253e-08
## 65 2.651253e-08
## 66 2.651253e-08
## 67 2.651253e-08
## 68 2.651253e-08
## 69 2.651253e-08
## 70 2.651253e-08
## 71 2.651253e-08
## 72 2.651253e-08
## 73 2.651253e-08
## 74 2.651253e-08
## 75 2.651253e-08
## 76 2.651253e-08
## 77 2.651253e-08
## 78 2.651253e-08
## 79 2.651253e-08
## 80 2.651253e-08
## 81 2.651253e-08
## 82 2.651253e-08
## 83 2.651253e-08
## 84 2.651253e-08
## 85 2.651253e-08
## 86 2.651253e-08
## 87 2.651253e-08
## 88 2.651253e-08
## 89 2.651253e-08
## 90 2.651253e-08
## 91 2.651253e-08
## 92 2.651253e-08
## 93 8.611958e-07
## 94 2.651253e-08
## 95 2.651253e-08
## 96 2.651253e-08
## 97 2.651253e-08
## 98 2.651253e-08
## 99 2.651253e-08
## 100 2.651253e-08
## 101 2.651253e-08
## 102 2.651253e-08
## 103 2.651253e-08
## 104 2.651253e-08
## 105 2.651253e-08
## 106 2.651253e-08
## 107 2.651253e-08
## 108 2.651253e-08
## 109 2.651253e-08
## 110 2.651253e-08
## 111 2.651253e-08
## 112 2.651253e-08
## 113 2.651253e-08
## 114 2.651253e-08
## 115 2.651253e-08
## 116 2.651253e-08
## 117 2.651253e-08
## 118 2.651253e-08
## 119 2.651253e-08
## 120 2.651253e-08
## 121 2.651253e-08
## 122 2.651253e-08
## 123 2.651253e-08
## 124 2.651253e-08
## 125 2.651253e-08
## 126 2.651253e-08
## 127 2.651253e-08
## 128 2.651253e-08
## 129 2.651253e-08
## 130 2.651253e-08
## 131 2.651253e-08
## 132 1.132505e-07
## 133 6.038130e-08245 SNPs pass genome-wide significance, 8 index SNPs identified (chr 1-5, 8, 12, 14), supporting SNPs are present for index on chr 1, 4, 5, 8.
R ACD
r_acd_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$R.AC.Depth, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
r_acd_gwas <- na.omit(r_acd_gwas)
r_acd_filtered <- r_acd_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
r_acd_meff <- r_acd_filtered %>% filter(p < 1.84e-7)
r_acd_sig <- do.call(rbind, lapply(split(r_acd_meff,r_acd_meff$chr), function(x) {return(x[which.min(x$p),])}))
r_acd_res <- NULL
for (i in r_acd_sig$id) {
snpID <- i
snpCHR <- r_acd_filtered[r_acd_filtered$id == snpID,]$chr
snpPOS <- r_acd_filtered[r_acd_filtered$id ==snpID,]$pos
sig.peak <- r_acd_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
r_acd_res <- rbind(r_acd_res, sig.peak)
}
r_acd_res## chr pos id A1 A2 freqA2 h2 LRT p
## 1 11 87921800 rs17151049 C T 0.9362319 0.05135354 33.25732 8.07353e-091 SNP passed genome-wide significance, which is the index SNP, and no supporting SNPs are present.
R Cyl Pre-dilate
r_cyl_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$R.Cyl..pre.dilate, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
r_cyl_gwas <- na.omit(r_cyl_gwas)
r_cyl_filtered <- r_cyl_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
r_cyl_meff <- r_cyl_filtered %>% filter(p < 1.84e-7)
r_cyl_sig <- do.call(rbind, lapply(split(r_cyl_meff,r_cyl_meff$chr), function(x) {return(x[which.min(x$p),])}))
r_cyl_res <- NULL
for (i in r_cyl_sig$id) {
snpID <- i
snpCHR <- r_cyl_filtered[r_cyl_filtered$id == snpID,]$chr
snpPOS <- r_cyl_filtered[r_cyl_filtered$id ==snpID,]$pos
sig.peak <- r_cyl_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
r_cyl_res <- rbind(r_cyl_res, sig.peak)
}
r_cyl_res## chr pos id A1 A2 freqA2 h2 LRT
## 1 1 205916566 rs72752923 C A 0.9782609 0.3590877 38.66094
## 2 1 205916729 rs16830364 G A 0.9782609 0.3590877 38.66094
## 3 1 205916931 rs60255052 C T 0.9811594 0.3024487 45.24602
## 4 1 205917041 rs60716530 C T 0.9782609 0.3590877 38.66094
## 5 1 205917115 rs60644810 G A 0.9782609 0.3590877 38.66094
## 6 1 205917248 rs35694044 A T 0.9782609 0.3590877 38.66094
## 7 1 205917652 rs16830370 T C 0.9782609 0.3590877 38.66094
## 8 1 205918853 rs16856462 C T 0.9782609 0.3590877 38.66094
## 9 1 205919195 rs16856468 G A 0.9782609 0.3590877 38.66094
## 10 1 205919303 rs60001177 T C 0.9782609 0.3590877 38.66094
## 11 1 205919401 rs12723666 A G 0.9782609 0.3590877 38.66094
## 12 1 205920201 rs16856470 T C 0.9811594 0.3024487 45.24602
## 13 1 205920404 rs16856473 A G 0.9811594 0.3024487 45.24602
## 14 1 205922403 rs68189466 G A 0.9797101 0.3328177 44.03053
## 15 1 205922720 rs35648260 G T 0.9797101 0.3328177 44.03053
## 16 1 205922775 rs35360452 G T 0.9797101 0.3328177 44.03053
## 17 1 205925474 rs12727528 A G 0.9797101 0.3328177 44.03053
## 18 1 205935183 rs1891309 G A 0.9782609 0.3509032 38.14269
## 19 1 205935330 rs1891310 T G 0.9782609 0.3509032 38.14269
## 20 1 205936240 rs1473537 T C 0.9739130 0.3988371 31.58795
## 21 1 205942026 rs72752928 T C 0.9782609 0.3509032 38.14269
## 22 1 205943691 rs66593238 T C 0.9782609 0.3509032 38.14269
## 23 1 205944627 rs9438407 T G 0.9782609 0.3509032 38.14269
## 24 1 205945388 rs12741299 T C 0.9782609 0.3509032 38.14269
## 25 1 205946647 rs34265780 T C 0.9782609 0.3509032 38.14269
## 26 2 22752117 rs72793052 C T 0.9768116 0.3145422 46.82150
## 27 2 22759734 rs72793060 C G 0.9579710 0.4074121 29.26252
## 28 2 22763823 rs72793066 T C 0.9579710 0.4074121 29.26252
## 29 2 22764837 rs72793070 C G 0.9579710 0.4074121 29.26252
## 30 2 22770868 rs4353679 C T 0.9579710 0.4074121 29.26252
## 31 2 22771019 rs4343495 T C 0.9579710 0.4074121 29.26252
## 32 2 22778013 rs72793089 A T 0.9579710 0.4074121 29.26252
## 33 2 22780281 rs10187240 C T 0.9579710 0.4074121 29.26252
## 34 2 22786683 rs72794813 C T 0.9579710 0.4074121 29.26252
## 35 2 22792883 rs6719784 T A 0.9579710 0.4074121 29.26252
## 36 3 42006157 rs71315517 G C 0.9869565 0.3205628 32.90971
## 37 4 119362510 rs112314510 A G 0.9855072 0.2827593 55.28065
## 38 4 119362552 rs111968273 T A 0.9855072 0.2827593 55.28065
## 39 4 119367677 rs113059419 A G 0.9869565 0.2209770 60.08399
## 40 4 119372303 rs112760591 G A 0.9855072 0.2827593 55.28065
## 41 4 119372480 rs111609258 C G 0.9855072 0.2827593 55.28065
## 42 4 119378224 rs147602981 G A 0.9855072 0.2827593 55.28065
## 43 4 119381167 rs143847948 A C 0.9855072 0.2827593 55.28065
## 44 4 119390257 rs113224532 T C 0.9855072 0.2827593 55.28065
## 45 4 119392279 rs117856633 C A 0.9855072 0.2827593 55.28065
## 46 4 119398681 rs113825627 C G 0.9855072 0.2827593 55.28065
## 47 4 119403429 rs112414671 A G 0.9869565 0.2209770 60.08399
## 48 4 119403485 rs185357281 A G 0.9869565 0.3262477 34.30287
## 49 4 119404439 rs183181597 A G 0.9855072 0.2827593 55.28065
## 50 4 119404927 rs113317707 C A 0.9855072 0.2827593 55.28065
## 51 4 119408454 rs184703141 T C 0.9855072 0.2827593 55.28065
## 52 5 33168945 rs113442983 T C 0.9898551 0.4220320 61.41397
## 53 7 150609580 rs12668363 C T 0.9869565 0.4435804 36.99348
## 54 8 80306741 rs111864836 G T 0.9884058 0.3773594 39.14554
## 55 8 80306859 rs113627660 G C 0.9884058 0.3773594 39.14554
## 56 8 80306990 rs7825643 G T 0.9724638 0.5238540 19.63518
## 57 8 80307293 rs7845792 A G 0.9884058 0.3773594 39.14554
## 58 8 80307388 rs7845575 G A 0.9869565 0.3990852 33.19626
## 59 8 80307700 rs114654811 C T 0.9884058 0.3773594 39.14554
## 60 8 80307701 rs115278078 A T 0.9884058 0.3773594 39.14554
## 61 8 80307837 rs79018076 T C 0.9884058 0.3773594 39.14554
## 62 8 80308098 rs112501384 G C 0.9884058 0.3773594 39.14554
## 63 8 80309142 rs60539023 G A 0.9724638 0.5238540 19.63518
## 64 8 80309305 rs11996376 A G 0.9884058 0.3773594 39.14554
## 65 8 80309598 rs79431653 C G 0.9884058 0.3773594 39.14554
## 66 8 80309626 rs11996450 T C 0.9884058 0.3773594 39.14554
## 67 8 80310193 rs60741023 C G 0.9884058 0.3773594 39.14554
## 68 8 80310485 rs7844286 C T 0.9884058 0.3773594 39.14554
## 69 8 80310716 rs7844696 A T 0.9884058 0.3773594 39.14554
## 70 8 80310720 rs7826434 G A 0.9884058 0.3773594 39.14554
## 71 8 80311242 rs80031189 C T 0.9884058 0.3773594 39.14554
## 72 8 80311252 rs113823684 A G 0.9884058 0.3773594 39.14554
## 73 8 80311311 rs61300312 A C 0.9724638 0.5238540 19.63518
## 74 8 80311329 rs142907856 A G 0.9884058 0.3773594 39.14554
## 75 8 80311457 rs112582272 A G 0.9884058 0.3773594 39.14554
## 76 8 80311580 rs116773209 G A 0.9884058 0.3773594 39.14554
## 77 8 80311736 rs113314270 G T 0.9884058 0.3773594 39.14554
## 78 8 80311746 rs73261635 G A 0.9724638 0.5238540 19.63518
## 79 8 80311838 rs117693425 A G 0.9884058 0.3773594 39.14554
## 80 8 80312291 rs11988873 C T 0.9884058 0.3773594 39.14554
## 81 8 80312345 rs11988904 A T 0.9884058 0.3773594 39.14554
## 82 8 80312623 rs36051398 A C 0.9884058 0.3773594 39.14554
## 83 8 80313237 rs73261640 G A 0.9724638 0.5238540 19.63518
## 84 8 80313751 rs114426401 T C 0.9884058 0.3773594 39.14554
## 85 8 80314228 rs74981396 G A 0.9884058 0.3773594 39.14554
## 86 8 80317028 rs11998344 T G 0.9884058 0.3773594 39.14554
## 87 8 80317208 rs113244900 C T 0.9884058 0.3773594 39.14554
## 88 8 80318583 rs57246091 A G 0.9884058 0.3773594 39.14554
## 89 8 80318643 rs113901603 G A 0.9884058 0.3773594 39.14554
## 90 8 80319691 rs113718590 A G 0.9884058 0.3773594 39.14554
## 91 8 80319794 rs111833373 C T 0.9724638 0.5238540 19.63518
## 92 8 80320713 rs11987997 A G 0.9884058 0.3773594 39.14554
## 93 8 80321002 rs111527437 T A 0.9884058 0.3773594 39.14554
## 94 8 80321694 rs112815920 G C 0.9884058 0.3773594 39.14554
## 95 8 80323890 rs11998156 C A 0.9884058 0.3773594 39.14554
## 96 8 80323964 rs16907573 G A 0.9884058 0.3773594 39.14554
## 97 8 80324156 rs111257240 C T 0.9884058 0.3773594 39.14554
## 98 8 80325047 rs113437388 T C 0.9884058 0.3773594 39.14554
## 99 8 80325311 rs73261674 G C 0.9724638 0.5238540 19.63518
## 100 8 80326033 rs111370206 G A 0.9884058 0.3773594 39.14554
## 101 8 80326181 rs73261679 A C 0.9724638 0.5238540 19.63518
## 102 8 80326935 rs147955676 A G 0.9884058 0.3773594 39.14554
## 103 8 80326985 rs61039050 A C 0.9724638 0.5238540 19.63518
## 104 8 80327347 rs7840954 C T 0.9724638 0.5238540 19.63518
## 105 8 80327348 rs7822886 A G 0.9724638 0.5238540 19.63518
## 106 8 80327442 rs7841095 C T 0.9884058 0.3773594 39.14554
## 107 8 80327549 rs7822828 C A 0.9884058 0.3773594 39.14554
## 108 8 80327674 rs7841418 C T 0.9724638 0.5238540 19.63518
## 109 8 80327732 rs7823481 C G 0.9884058 0.3773594 39.14554
## 110 8 80328450 rs11990649 A G 0.9884058 0.3773594 39.14554
## 111 8 80329801 rs56960849 A G 0.9884058 0.3773594 39.14554
## 112 8 80330197 rs11995624 C T 0.9884058 0.3773594 39.14554
## 113 8 80330467 rs7837761 A G 0.9869565 0.3990852 33.19626
## 114 8 80332180 rs113042618 T C 0.9884058 0.3773594 39.14554
## 115 8 80332423 rs7001142 G T 0.9884058 0.3773594 39.14554
## 116 8 80332520 rs6980915 G A 0.9884058 0.3773594 39.14554
## 117 8 80332901 rs6473220 T C 0.9884058 0.3773594 39.14554
## 118 8 80332907 rs6473221 A G 0.9884058 0.3773594 39.14554
## 119 8 80333316 rs7835862 C T 0.9884058 0.3773594 39.14554
## 120 8 80333340 rs7817696 A G 0.9884058 0.3773594 39.14554
## 121 8 80333506 rs7817634 T C 0.9884058 0.3773594 39.14554
## 122 8 80333599 rs57419267 C T 0.9884058 0.3773594 39.14554
## 123 8 80333823 rs59130219 C T 0.9884058 0.3773594 39.14554
## 124 8 80334098 rs73691385 T A 0.9884058 0.3773594 39.14554
## 125 8 80334328 rs7840559 C T 0.9884058 0.3773594 39.14554
## 126 8 80334334 rs7822177 G A 0.9884058 0.3773594 39.14554
## 127 8 80334582 rs111631456 A G 0.9884058 0.3773594 39.14554
## 128 8 80334982 rs58109903 T C 0.9884058 0.3773594 39.14554
## 129 8 80335583 rs73691388 G A 0.9884058 0.3773594 39.14554
## 130 8 80336124 rs7837108 T C 0.9884058 0.3773594 39.14554
## 131 8 80336300 rs7840857 T G 0.9884058 0.3773594 39.14554
## 132 8 80336310 rs7840861 T G 0.9884058 0.3773594 39.14554
## 133 8 80337292 rs111888115 T C 0.9884058 0.3773594 39.14554
## 134 8 80337308 rs56871558 T C 0.9884058 0.3773594 39.14554
## 135 8 80337408 rs56116331 A G 0.9884058 0.3773594 39.14554
## 136 8 80337443 rs58592997 T C 0.9884058 0.3773594 39.14554
## 137 8 80337629 rs76783901 A G 0.9884058 0.3773594 39.14554
## 138 8 80337634 rs74468856 G A 0.9884058 0.3773594 39.14554
## 139 8 80337985 rs73691394 C A 0.9884058 0.3773594 39.14554
## 140 8 80338076 rs73691395 T C 0.9884058 0.3773594 39.14554
## 141 8 80338219 rs73691397 C G 0.9884058 0.3773594 39.14554
## 142 8 80338255 rs73691398 G A 0.9884058 0.3773594 39.14554
## 143 8 80338835 rs58958046 A G 0.9884058 0.3773594 39.14554
## 144 8 80338910 rs58786240 C T 0.9884058 0.3773594 39.14554
## 145 8 80338955 rs76867788 C T 0.9884058 0.3773594 39.14554
## 146 8 80339017 rs73691399 T C 0.9884058 0.3773594 39.14554
## 147 8 80339217 rs73691400 C G 0.9884058 0.3773594 39.14554
## 148 8 80339959 rs61233095 C A 0.9884058 0.3773594 39.14554
## 149 8 80340238 rs56408864 A T 0.9884058 0.3773594 39.14554
## 150 8 80340749 rs7826667 A G 0.9884058 0.3773594 39.14554
## 151 8 80341236 rs7000592 G C 0.9884058 0.3773594 39.14554
## 152 9 111071527 rs140186619 C G 0.9855072 0.4710464 21.52887
## 153 9 111075633 rs74647073 T C 0.9884058 0.4760068 33.56573
## 154 10 90323959 rs112690545 C T 0.9898551 0.4905849 39.14067
## 155 10 90325010 rs113836370 C T 0.9898551 0.4905849 39.14067
## 156 10 90325072 rs111559585 G A 0.9898551 0.4905849 39.14067
## 157 10 90325630 rs111374977 G A 0.9898551 0.4905849 39.14067
## 158 10 90327444 rs113290534 T C 0.9898551 0.4905849 39.14067
## 159 11 100721739 rs148096302 A G 0.9840580 0.3338903 26.94081
## 160 11 100769446 rs78598508 G A 0.9753623 0.2428895 42.11482
## 161 12 13790930 rs116962554 T C 0.9898551 0.3984131 29.03841
## 162 12 13793136 rs146599464 A G 0.9898551 0.3984131 29.03841
## 163 12 13800451 rs117584437 G C 0.9898551 0.3984131 29.03841
## 164 12 13802357 rs113017232 C T 0.9898551 0.3984131 29.03841
## 165 12 13802362 rs111823455 A C 0.9898551 0.3984131 29.03841
## 166 12 13807964 rs220584 A G 0.9898551 0.3984131 29.03841
## 167 13 94647114 rs61965613 A C 0.9898551 0.4545725 19.71557
## 168 13 94652507 rs61965632 T A 0.9898551 0.4545725 19.71557
## 169 13 94655446 rs61965634 T C 0.9898551 0.4545725 19.71557
## 170 13 94679031 rs4771891 G T 0.9594203 0.3708084 28.51995
## 171 14 77683279 rs117466773 C T 0.9884058 0.3483513 38.95078
## 172 14 77683756 rs146875663 A G 0.9884058 0.3483513 38.95078
## 173 14 77703768 rs140932637 G T 0.9898551 0.3297162 45.54160
## 174 16 63440590 rs141104955 G C 0.9898551 0.5038479 38.72335
## 175 17 78089009 rs150771315 G C 0.9826087 0.4413037 31.38887
## 176 18 50137976 rs73430360 G T 0.9855072 0.2151360 50.56739
## 177 19 53778042 rs56192182 C T 0.9884058 0.3885583 28.92266
## 178 20 43955922 rs6031258 A G 0.9855072 0.4790113 22.10547
## 179 20 43965564 rs73118275 A G 0.9884058 0.4436936 31.73982
## 180 20 43967430 rs73118278 T C 0.9884058 0.4436936 31.73982
## 181 20 43973892 rs67340628 T G 0.9884058 0.4436936 31.73982
## 182 22 33116757 rs16991802 A G 0.9768116 0.3814350 28.93202
## p
## 1 5.041979e-10
## 2 5.041979e-10
## 3 1.737732e-11
## 4 5.041979e-10
## 5 5.041979e-10
## 6 5.041979e-10
## 7 5.041979e-10
## 8 5.041979e-10
## 9 5.041979e-10
## 10 5.041979e-10
## 11 5.041979e-10
## 12 1.737732e-11
## 13 1.737732e-11
## 14 3.232940e-11
## 15 3.232940e-11
## 16 3.232940e-11
## 17 3.232940e-11
## 18 6.575564e-10
## 19 6.575564e-10
## 20 1.906085e-08
## 21 6.575564e-10
## 22 6.575564e-10
## 23 6.575564e-10
## 24 6.575564e-10
## 25 6.575564e-10
## 26 7.775581e-12
## 27 6.320647e-08
## 28 6.320647e-08
## 29 6.320647e-08
## 30 6.320647e-08
## 31 6.320647e-08
## 32 6.320647e-08
## 33 6.320647e-08
## 34 6.320647e-08
## 35 6.320647e-08
## 36 9.653973e-09
## 37 1.044923e-13
## 38 1.044923e-13
## 39 9.089454e-15
## 40 1.044923e-13
## 41 1.044923e-13
## 42 1.044923e-13
## 43 1.044923e-13
## 44 1.044923e-13
## 45 1.044923e-13
## 46 1.044923e-13
## 47 9.089454e-15
## 48 4.716851e-09
## 49 1.044923e-13
## 50 1.044923e-13
## 51 1.044923e-13
## 52 4.625179e-15
## 53 1.185247e-09
## 54 3.933614e-10
## 55 3.933614e-10
## 56 9.372753e-06
## 57 3.933614e-10
## 58 8.331061e-09
## 59 3.933614e-10
## 60 3.933614e-10
## 61 3.933614e-10
## 62 3.933614e-10
## 63 9.372753e-06
## 64 3.933614e-10
## 65 3.933614e-10
## 66 3.933614e-10
## 67 3.933614e-10
## 68 3.933614e-10
## 69 3.933614e-10
## 70 3.933614e-10
## 71 3.933614e-10
## 72 3.933614e-10
## 73 9.372753e-06
## 74 3.933614e-10
## 75 3.933614e-10
## 76 3.933614e-10
## 77 3.933614e-10
## 78 9.372753e-06
## 79 3.933614e-10
## 80 3.933614e-10
## 81 3.933614e-10
## 82 3.933614e-10
## 83 9.372753e-06
## 84 3.933614e-10
## 85 3.933614e-10
## 86 3.933614e-10
## 87 3.933614e-10
## 88 3.933614e-10
## 89 3.933614e-10
## 90 3.933614e-10
## 91 9.372753e-06
## 92 3.933614e-10
## 93 3.933614e-10
## 94 3.933614e-10
## 95 3.933614e-10
## 96 3.933614e-10
## 97 3.933614e-10
## 98 3.933614e-10
## 99 9.372753e-06
## 100 3.933614e-10
## 101 9.372753e-06
## 102 3.933614e-10
## 103 9.372753e-06
## 104 9.372753e-06
## 105 9.372753e-06
## 106 3.933614e-10
## 107 3.933614e-10
## 108 9.372753e-06
## 109 3.933614e-10
## 110 3.933614e-10
## 111 3.933614e-10
## 112 3.933614e-10
## 113 8.331061e-09
## 114 3.933614e-10
## 115 3.933614e-10
## 116 3.933614e-10
## 117 3.933614e-10
## 118 3.933614e-10
## 119 3.933614e-10
## 120 3.933614e-10
## 121 3.933614e-10
## 122 3.933614e-10
## 123 3.933614e-10
## 124 3.933614e-10
## 125 3.933614e-10
## 126 3.933614e-10
## 127 3.933614e-10
## 128 3.933614e-10
## 129 3.933614e-10
## 130 3.933614e-10
## 131 3.933614e-10
## 132 3.933614e-10
## 133 3.933614e-10
## 134 3.933614e-10
## 135 3.933614e-10
## 136 3.933614e-10
## 137 3.933614e-10
## 138 3.933614e-10
## 139 3.933614e-10
## 140 3.933614e-10
## 141 3.933614e-10
## 142 3.933614e-10
## 143 3.933614e-10
## 144 3.933614e-10
## 145 3.933614e-10
## 146 3.933614e-10
## 147 3.933614e-10
## 148 3.933614e-10
## 149 3.933614e-10
## 150 3.933614e-10
## 151 3.933614e-10
## 152 3.485412e-06
## 153 6.889610e-09
## 154 3.943437e-10
## 155 3.943437e-10
## 156 3.943437e-10
## 157 3.943437e-10
## 158 3.943437e-10
## 159 2.097822e-07
## 160 8.606828e-11
## 161 7.095735e-08
## 162 7.095735e-08
## 163 7.095735e-08
## 164 7.095735e-08
## 165 7.095735e-08
## 166 7.095735e-08
## 167 8.986609e-06
## 168 8.986609e-06
## 169 8.986609e-06
## 170 9.273778e-08
## 171 4.346271e-10
## 172 4.346271e-10
## 173 1.494309e-11
## 174 4.883314e-10
## 175 2.111881e-08
## 176 1.151425e-12
## 177 7.532646e-08
## 178 2.580737e-06
## 179 1.762712e-08
## 180 1.762712e-08
## 181 1.762712e-08
## 182 7.496329e-08394 SNPs pass genome-wide significance, 19 index SNPs identified (chr 1-5, 7-14, 16-20, 22), supporting SNPs present for index on chr 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 20.
UVAF
uvaf_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$totaluvafmm, method="lmm", test = "lrt", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
uvaf_gwas <- na.omit(uvaf_gwas)
uvaf_filtered <- uvaf_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
uvaf_meff <- uvaf_filtered %>% filter(p < 1.84e-7)
uvaf_sig <- do.call(rbind, lapply(split(uvaf_meff,uvaf_meff$chr), function(x) {return(x[which.min(x$p),])}))
uvaf_res <- NULL
for (i in uvaf_sig$id) {
snpID <- i
snpCHR <- uvaf_filtered[uvaf_filtered$id == snpID,]$chr
snpPOS <- uvaf_filtered[uvaf_filtered$id ==snpID,]$pos
sig.peak <- uvaf_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
uvaf_res <- rbind(uvaf_res, sig.peak)
}
uvaf_res## chr pos id A1 A2 freqA2 h2 LRT
## 1 7 107578936 rs191522213 G C 0.9884058 0.3552125 37.34589
## 2 8 34731289 rs116937259 C T 0.9884058 0.3505130 33.58738
## 3 8 34738629 rs141115618 C G 0.9898551 0.3528903 26.03643
## 4 8 34743083 rs192922472 T C 0.9884058 0.3505130 33.58738
## 5 9 68580538 rs6560237 C T 0.9753623 0.3167411 25.77905
## 6 9 68581265 rs7048633 T C 0.9753623 0.3167411 25.77905
## 7 9 68583308 rs71501771 T A 0.9753623 0.3167411 25.77905
## 8 9 68586048 rs35551873 T C 0.9753623 0.3167411 25.77905
## 9 9 68586254 rs7045561 G A 0.9753623 0.3167411 25.77905
## 10 9 68587181 rs13288798 G T 0.9753623 0.3167411 25.77905
## 11 9 68587313 rs13284137 G A 0.9753623 0.3167411 25.77905
## 12 9 68588522 rs139047286 C T 0.9753623 0.3167411 25.77905
## 13 9 68588999 rs7859065 C T 0.9753623 0.3167411 25.77905
## 14 9 68594362 rs13290124 A G 0.9753623 0.3167411 25.77905
## 15 9 68595978 rs10511959 A G 0.9753623 0.3167411 25.77905
## 16 9 68597806 rs34412731 T C 0.9753623 0.3167411 25.77905
## 17 9 68599834 rs12004993 G A 0.9753623 0.3167411 25.77905
## 18 9 68605388 rs76930250 G C 0.9753623 0.3167411 25.77905
## 19 9 68605806 rs13287094 A G 0.9753623 0.3167411 25.77905
## 20 9 68608085 rs34921768 G A 0.9753623 0.3167411 25.77905
## 21 9 68608420 rs13299492 A G 0.9753623 0.3167411 25.77905
## 22 9 68612655 rs34344868 A G 0.9753623 0.3167411 25.77905
## 23 9 68615281 rs34805084 A G 0.9739130 0.3101203 21.49526
## 24 9 68618011 rs71501772 G C 0.9739130 0.3101203 21.49526
## 25 9 68618330 rs34763246 T C 0.9739130 0.3101203 21.49526
## 26 9 68619315 rs34436601 T C 0.9739130 0.3101203 21.49526
## 27 9 68621728 rs13289515 C G 0.9739130 0.3101203 21.49526
## 28 9 68624185 rs117741244 T C 0.9811594 0.2846828 34.07407
## 29 9 68629924 rs117987088 T C 0.9811594 0.2846828 34.07407
## 30 10 103760600 rs56309638 C T 0.9478261 0.2710545 20.68595
## 31 10 103760666 rs56275413 T C 0.9478261 0.2710545 20.68595
## 32 10 103762582 rs4918047 T C 0.9478261 0.2710545 20.68595
## 33 10 103763262 rs55760245 T C 0.9478261 0.2710545 20.68595
## 34 10 103763409 rs56178332 G C 0.9478261 0.2710545 20.68595
## 35 10 103764487 rs9665617 C T 0.9478261 0.2710545 20.68595
## 36 10 103764550 rs9665618 A T 0.9478261 0.2710545 20.68595
## 37 10 103765222 rs56030972 T C 0.9478261 0.2710545 20.68595
## 38 10 103767403 rs55909417 C A 0.9463768 0.2526346 25.21397
## 39 10 103768946 rs72817647 T C 0.9463768 0.2526346 25.21397
## 40 10 103769861 rs4917399 G A 0.9463768 0.2526346 25.21397
## 41 10 103769986 rs17115934 T C 0.9463768 0.2526346 25.21397
## 42 10 103771232 rs911546 A C 0.9463768 0.2526346 25.21397
## 43 10 103771521 rs11191800 A G 0.9463768 0.2526346 25.21397
## 44 10 103771634 rs2013456 T C 0.9478261 0.2739220 28.28936
## 45 10 103771936 rs911544 A G 0.9463768 0.2526346 25.21397
## 46 10 103773143 rs112836951 A G 0.9478261 0.2710545 20.68595
## 47 10 103773216 rs112995165 T C 0.9478261 0.2558203 27.64235
## 48 10 103774251 rs55908118 G A 0.9478261 0.2710545 20.68595
## 49 10 103775289 rs11191803 C T 0.9463768 0.2526346 25.21397
## p
## 1 9.892938e-10
## 2 6.813328e-09
## 3 3.350354e-07
## 4 6.813328e-09
## 5 3.828208e-07
## 6 3.828208e-07
## 7 3.828208e-07
## 8 3.828208e-07
## 9 3.828208e-07
## 10 3.828208e-07
## 11 3.828208e-07
## 12 3.828208e-07
## 13 3.828208e-07
## 14 3.828208e-07
## 15 3.828208e-07
## 16 3.828208e-07
## 17 3.828208e-07
## 18 3.828208e-07
## 19 3.828208e-07
## 20 3.828208e-07
## 21 3.828208e-07
## 22 3.828208e-07
## 23 3.547037e-06
## 24 3.547037e-06
## 25 3.547037e-06
## 26 3.547037e-06
## 27 3.547037e-06
## 28 5.305342e-09
## 29 5.305342e-09
## 30 5.411148e-06
## 31 5.411148e-06
## 32 5.411148e-06
## 33 5.411148e-06
## 34 5.411148e-06
## 35 5.411148e-06
## 36 5.411148e-06
## 37 5.411148e-06
## 38 5.130912e-07
## 39 5.130912e-07
## 40 5.130912e-07
## 41 5.130912e-07
## 42 5.130912e-07
## 43 5.130912e-07
## 44 1.044685e-07
## 45 5.130912e-07
## 46 5.411148e-06
## 47 1.459481e-07
## 48 5.411148e-06
## 49 5.130912e-07write.csv(uvaf_res, 'C:/Users/Martha/Documents/Honours/Project/honours.project/Data/gwas_filter/uvaf_res.csv')7 SNPs pass genome-wide significance, 4 index SNPs identified (chr 7, 8, 9, 10), supporting SNPs present for index on chr 8, 9, 10.
By identifying the index SNPs that have supporting SNPs passing the suggestive line (p < 1e-5), I eliminated three traits: L ACD, L CDR, and R ACD. Evidently, even in the other traits, not all index SNPs have supporting SNPs. Although the lack of supporting SNPs does not necessarily mean that they are false positives, their presence indicates robustness of the signigicant SNPs. And for the scope of this project, we do not have the capacity to determine whether any of the other significant hits without supporting SNPs are true. Therefore, I am only reporting the index SNPs that are well-supported.
l_KvalH_gwas <- association.test(merged_nies_210818, nies_heritable_pheno$L.K.value.H, method="lm", test = "wald", K = merged_nies_GRM, eigenK = merged_nies_eiK, p = 2)
l_KvalH_gwas <- na.omit(l_KvalH_gwas)
l_kvalH_filtered <- l_KvalH_gwas %>% filter(-log10(p)>1) %>% filter(freqA2 < 0.99)
l_kvalH_meff <- l_kvalH_filtered %>% filter(p < 1.84e-7)
l_kvalH_sig <- do.call(rbind, lapply(split(l_kvalH_meff,l_kvalH_meff$chr), function(x) {return(x[which.min(x$p),])}))
l_kvalH_res <- NULL
for (i in l_kvalH_sig$id) {
snpID <- i
snpCHR <- l_kvalH_filtered[l_kvalH_filtered$id == snpID,]$chr
snpPOS <- l_kvalH_filtered[l_kvalH_filtered$id ==snpID,]$pos
sig.peak <- l_kvalH_filtered %>%
filter(chr == snpCHR) %>%
filter(pos > snpPOS - 50000) %>%
filter(pos < snpPOS + 50000) %>%
filter(p < 1e-5)
l_kvalH_res <- rbind(l_kvalH_res, sig.peak)
}
l_kvalH_res## chr pos id A1 A2 freqA2 beta sd
## 1 2 176830012 rs72940750 C T 0.9898551 3.681223 0.6028117
## 2 2 176831387 rs7576095 A G 0.9898551 3.681223 0.6028117
## 3 2 176832679 rs6758571 G A 0.9898551 3.681223 0.6028117
## 4 2 176833429 rs139727961 G A 0.9898551 3.681223 0.6028117
## 5 2 176839936 rs72940766 A T 0.9898551 3.681223 0.6028117
## 6 2 176840625 rs72940776 T C 0.9898551 3.681223 0.6028117
## 7 2 176840683 rs72940781 C G 0.9898551 3.681223 0.6028117
## 8 2 176841189 rs6715723 T A 0.9898551 3.681223 0.6028117
## 9 3 77739700 rs1163757 A G 0.9869565 3.221804 0.5333681
## 10 6 82425908 rs73481987 C T 0.9753623 1.917424 0.4054810
## 11 6 82442490 rs114928787 T C 0.9855072 3.173559 0.4545536
## 12 6 82442833 rs116172930 C A 0.9855072 3.173559 0.4545536
## 13 6 82443802 rs74436554 C T 0.9855072 3.173559 0.4545536
## 14 6 82444791 rs78056249 C G 0.9855072 3.173559 0.4545536
## 15 6 82445716 rs77941466 C T 0.9855072 3.173559 0.4545536
## 16 6 82447004 rs116461493 T C 0.9855072 3.173559 0.4545536
## 17 6 82447732 rs77666578 G A 0.9855072 3.173559 0.4545536
## 18 6 82451563 rs75189229 A G 0.9855072 3.173559 0.4545536
## 19 6 82453938 rs117178778 A G 0.9855072 3.173559 0.4545536
## 20 6 82454058 rs116246536 T G 0.9855072 3.173559 0.4545536
## 21 6 82454140 rs78427866 A G 0.9855072 3.173559 0.4545536
## 22 6 82454380 rs147257041 A G 0.9855072 3.173559 0.4545536
## 23 6 82454449 rs140711073 T C 0.9855072 3.173559 0.4545536
## 24 6 82454505 rs142248448 T C 0.9855072 3.173559 0.4545536
## 25 6 82454620 rs114442506 A G 0.9855072 3.173559 0.4545536
## 26 6 82456537 rs145558293 A G 0.9855072 3.173559 0.4545536
## 27 6 82458393 rs77391407 C T 0.9855072 3.173559 0.4545536
## 28 6 82458546 rs77103853 G C 0.9855072 3.173559 0.4545536
## 29 6 82459011 rs115096710 T C 0.9855072 3.173559 0.4545536
## 30 6 82459713 rs77245672 G C 0.9855072 3.173559 0.4545536
## 31 6 82459810 rs77599496 T A 0.9855072 3.173559 0.4545536
## 32 6 82459890 rs77598967 G A 0.9855072 3.173559 0.4545536
## 33 6 82460167 rs115847999 C G 0.9855072 3.173559 0.4545536
## 34 6 82460379 rs116730626 G A 0.9855072 3.173559 0.4545536
## 35 6 82460650 rs149355051 G T 0.9855072 3.173559 0.4545536
## 36 6 82462126 rs76856243 T C 0.9855072 3.173559 0.4545536
## 37 6 82462603 rs6933239 C T 0.9855072 3.173559 0.4545536
## 38 6 82462992 rs6911216 A C 0.9855072 3.173559 0.4545536
## 39 6 82465617 rs6928806 A C 0.9855072 3.173559 0.4545536
## 40 6 82466574 rs74404091 C T 0.9855072 3.173559 0.4545536
## 41 6 82466715 rs79358384 G A 0.9855072 3.173559 0.4545536
## 42 6 82467200 rs77721025 A C 0.9855072 3.173559 0.4545536
## 43 6 82467706 rs116423281 A G 0.9855072 3.173559 0.4545536
## 44 6 82467953 rs142216660 T C 0.9855072 3.173559 0.4545536
## 45 6 82467988 rs140099919 A G 0.9855072 3.173559 0.4545536
## 46 6 82468668 rs78941585 G A 0.9855072 3.173559 0.4545536
## 47 6 82468774 rs75228268 A T 0.9855072 3.173559 0.4545536
## 48 6 82469116 rs77552654 T A 0.9855072 3.173559 0.4545536
## 49 6 82470649 rs149706908 G T 0.9855072 3.173559 0.4545536
## 50 6 82470651 rs144623191 T C 0.9855072 3.173559 0.4545536
## 51 6 82470859 rs192614396 C A 0.9855072 3.173559 0.4545536
## 52 6 82471119 rs151156468 C T 0.9855072 3.173559 0.4545536
## 53 6 82471338 rs140554533 A G 0.9855072 3.173559 0.4545536
## 54 6 82471381 rs150446760 C G 0.9855072 3.173559 0.4545536
## 55 6 82471679 rs138339145 T C 0.9855072 3.173559 0.4545536
## 56 6 82472140 rs142089466 T C 0.9855072 3.173559 0.4545536
## 57 6 82473676 rs147151928 G C 0.9855072 3.173559 0.4545536
## 58 6 82473679 rs140298049 C T 0.9855072 3.173559 0.4545536
## 59 6 82473688 rs149655171 A G 0.9855072 3.173559 0.4545536
## 60 6 82474468 rs146864360 T C 0.9855072 3.173559 0.4545536
## 61 6 82474648 rs140520501 C T 0.9855072 3.173559 0.4545536
## 62 6 82474867 rs150394443 T C 0.9855072 3.173559 0.4545536
## 63 6 82475320 rs143579868 A T 0.9855072 3.173559 0.4545536
## 64 6 82475696 rs115741750 C T 0.9855072 3.173559 0.4545536
## 65 6 82477810 rs77406497 T C 0.9855072 3.173559 0.4545536
## 66 6 82478378 rs115813741 T G 0.9855072 3.173559 0.4545536
## 67 6 82478650 rs78900243 G A 0.9855072 3.173559 0.4545536
## 68 6 82478870 rs76557363 T G 0.9855072 3.173559 0.4545536
## 69 6 82479264 rs77943130 T G 0.9855072 3.173559 0.4545536
## 70 6 82479546 rs115245280 A G 0.9855072 3.173559 0.4545536
## 71 6 82479664 rs75910615 A G 0.9855072 3.173559 0.4545536
## 72 6 82480370 rs76438934 A G 0.9855072 3.173559 0.4545536
## 73 6 82481986 rs115034961 A C 0.9855072 3.173559 0.4545536
## 74 6 82482183 rs79967481 G A 0.9855072 3.173559 0.4545536
## 75 6 82482254 rs116699765 T C 0.9855072 3.173559 0.4545536
## 76 6 82483125 rs78639250 T C 0.9855072 3.173559 0.4545536
## 77 6 82483522 rs75763492 A G 0.9855072 3.173559 0.4545536
## 78 6 82483898 rs76617768 T C 0.9855072 3.173559 0.4545536
## 79 6 82484287 rs76652063 C A 0.9855072 3.173559 0.4545536
## 80 6 82484758 rs114024754 A G 0.9855072 3.173559 0.4545536
## 81 6 82485370 rs79031996 C G 0.9855072 3.173559 0.4545536
## 82 6 82485916 rs77517398 C T 0.9855072 3.173559 0.4545536
## 83 6 82486863 rs80252551 A T 0.9855072 3.173559 0.4545536
## 84 6 82488997 rs114963095 G T 0.9855072 3.173559 0.4545536
## 85 6 82489053 rs77561386 C T 0.9855072 3.173559 0.4545536
## 86 6 82489164 rs76602861 A G 0.9855072 3.173559 0.4545536
## 87 6 82490178 rs79435750 A G 0.9855072 3.173559 0.4545536
## 88 6 82490367 rs80347071 C G 0.9855072 3.173559 0.4545536
## 89 6 82492170 rs74785531 C T 0.9855072 3.173559 0.4545536
## 90 6 82492233 rs74361967 C T 0.9855072 3.173559 0.4545536
## 91 6 82492321 rs75373608 A T 0.9855072 3.173559 0.4545536
## 92 10 64099069 rs74804993 G A 0.9826087 2.637507 0.4654519
## 93 16 13935176 rs1800067 A G 0.9550725 1.635103 0.2819104
## p
## 1 2.769829e-09
## 2 2.769829e-09
## 3 2.769829e-09
## 4 2.769829e-09
## 5 2.769829e-09
## 6 2.769829e-09
## 7 2.769829e-09
## 8 2.769829e-09
## 9 4.020056e-09
## 10 3.311531e-06
## 11 1.530777e-11
## 12 1.530777e-11
## 13 1.530777e-11
## 14 1.530777e-11
## 15 1.530777e-11
## 16 1.530777e-11
## 17 1.530777e-11
## 18 1.530777e-11
## 19 1.530777e-11
## 20 1.530777e-11
## 21 1.530777e-11
## 22 1.530777e-11
## 23 1.530777e-11
## 24 1.530777e-11
## 25 1.530777e-11
## 26 1.530777e-11
## 27 1.530777e-11
## 28 1.530777e-11
## 29 1.530777e-11
## 30 1.530777e-11
## 31 1.530777e-11
## 32 1.530777e-11
## 33 1.530777e-11
## 34 1.530777e-11
## 35 1.530777e-11
## 36 1.530777e-11
## 37 1.530777e-11
## 38 1.530777e-11
## 39 1.530777e-11
## 40 1.530777e-11
## 41 1.530777e-11
## 42 1.530777e-11
## 43 1.530777e-11
## 44 1.530777e-11
## 45 1.530777e-11
## 46 1.530777e-11
## 47 1.530777e-11
## 48 1.530777e-11
## 49 1.530777e-11
## 50 1.530777e-11
## 51 1.530777e-11
## 52 1.530777e-11
## 53 1.530777e-11
## 54 1.530777e-11
## 55 1.530777e-11
## 56 1.530777e-11
## 57 1.530777e-11
## 58 1.530777e-11
## 59 1.530777e-11
## 60 1.530777e-11
## 61 1.530777e-11
## 62 1.530777e-11
## 63 1.530777e-11
## 64 1.530777e-11
## 65 1.530777e-11
## 66 1.530777e-11
## 67 1.530777e-11
## 68 1.530777e-11
## 69 1.530777e-11
## 70 1.530777e-11
## 71 1.530777e-11
## 72 1.530777e-11
## 73 1.530777e-11
## 74 1.530777e-11
## 75 1.530777e-11
## 76 1.530777e-11
## 77 1.530777e-11
## 78 1.530777e-11
## 79 1.530777e-11
## 80 1.530777e-11
## 81 1.530777e-11
## 82 1.530777e-11
## 83 1.530777e-11
## 84 1.530777e-11
## 85 1.530777e-11
## 86 1.530777e-11
## 87 1.530777e-11
## 88 1.530777e-11
## 89 1.530777e-11
## 90 1.530777e-11
## 91 1.530777e-11
## 92 3.102948e-08
## 93 1.512997e-08